Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 32
Found at i:155877 original size:15 final size:15
Alignment explanation
Indices: 155830--155877 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
155820 TTAGAAATAA
155830 GAAATT-AAAGAAAT
1 GAAATTGAAAGAAAT
155844 GGAAATTGATAAGAAAT
1 -GAAATTGA-AAGAAAT
155861 GAAATTGAAAGAAAT
1 GAAATTGAAAGAAAT
155876 GA
1 GA
155878 TATCAAGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.48
16 9 0.29
17 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (15 bp):
GAAATTGAAAGAAAT
Found at i:156623 original size:29 final size:29
Alignment explanation
Indices: 156591--156652 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
156581 TGCACATGCT
*
156591 TGCATGATGCACATGGCAGCCTATATGAA
1 TGCATGATGCACATGGCAACCTATATGAA
*
156620 TGCATGATGCTCATGGCAACCTATATGAA
1 TGCATGATGCACATGGCAACCTATATGAA
156649 TGCA
1 TGCA
156653 CATGGGTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (29 bp):
TGCATGATGCACATGGCAACCTATATGAA
Found at i:159497 original size:17 final size:17
Alignment explanation
Indices: 159462--159497 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
159452 TTGCGTCGGC
*
159462 TATAGAAATGGTTAGGG
1 TATAGAAATGGATAGGG
*
159479 TATAGAAATGGATATGG
1 TATAGAAATGGATAGGG
159496 TA
1 TA
159498 AAGGTAGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (17 bp):
TATAGAAATGGATAGGG
Found at i:162945 original size:19 final size:21
Alignment explanation
Indices: 162923--162979 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
162913 AGAACCCCAG
162923 GGGGGTATCGATTCCCC-T-A
1 GGGGGTATCGATTCCCCTTAA
* *
162942 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGTATCGATTCCCCTT-AA
*
162964 GAGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
162980 TCTGCCCTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 15 0.50
20 1 0.03
22 14 0.47
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.25
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCTTAA
Found at i:162978 original size:22 final size:19
Alignment explanation
Indices: 162925--162979 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
162915 AACCCCAGGG
*
162925 GGGTATCGATTCCCCTAGG
1 GGGTATCGATTCCCCTAGA
* *
162944 GGGAATCGGTTCCCCTTCAAGA
1 GGGTATCGATTCCCC-T--AGA
162966 GGGTATCGATTCCC
1 GGGTATCGATTCCC
162980 TCTGCCCTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 13 0.46
20 1 0.04
22 14 0.50
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.25
Consensus pattern (19 bp):
GGGTATCGATTCCCCTAGA
Found at i:167647 original size:17 final size:16
Alignment explanation
Indices: 167627--167669 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
167617 TTTACTTCAC
167627 TTTTTCTTTTTCTTTGT
1 TTTTTCTTTTTCTTT-T
**
167644 TTTTGATTTTTCTTTT
1 TTTTTCTTTTTCTTTT
167660 TCTTTTCTTT
1 T-TTTTCTTT
167670 CTTTTTGCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTTCTTTT
Found at i:167975 original size:15 final size:14
Alignment explanation
Indices: 167931--167978 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 14
167921 TTAGAAATAA
167931 GAAATGAAAGAAAT
1 GAAATGAAAGAAAT
167945 GGAAATTGATAAGAAAT
1 -GAAA-TGA-AAGAAAT
167962 GAAATGGAAAGAAAT
1 GAAAT-GAAAGAAAT
167977 GA
1 GA
167979 TATCAAGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 14 0.47
16 9 0.30
17 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (14 bp):
GAAATGAAAGAAAT
Found at i:167975 original size:26 final size:24
Alignment explanation
Indices: 167927--167980 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 24
167917 TTAATTAGAA
167927 ATAAGAAATGAAAGAAATGGAAATTG
1 ATAAGAAATGAAAGAAA-GGAAA-TG
167953 ATAAGAAATGAAATGGAAA-GAAATG
1 ATAAGAAATGAAA--GAAAGGAAATG
167978 ATA
1 ATA
167981 TCAAGGTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 5 0.19
26 17 0.65
28 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (24 bp):
ATAAGAAATGAAAGAAAGGAAATG
Found at i:168526 original size:19 final size:19
Alignment explanation
Indices: 168502--168540 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
168492 ACATGATTTG
168502 TTTTAATGAAAATACATGA
1 TTTTAATGAAAATACATGA
*
168521 TTTTAATGAAGATACATGA
1 TTTTAATGAAAATACATGA
168540 T
1 T
168541 CTTGGCAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTTAATGAAAATACATGA
Found at i:171037 original size:2 final size:2
Alignment explanation
Indices: 171030--171064 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
171020 CGTCACCTTA
171030 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
171065 ATTATTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:171065 original size:8 final size:9
Alignment explanation
Indices: 171028--171075 Score: 57
Period size: 8 Copynumber: 5.6 Consensus size: 9
171018 TACGTCACCT
171028 TAATATATA
1 TAATATATA
171037 T-ATATATA
1 TAATATATA
171045 TATATATATA
1 TA-ATATATA
171055 TAAT-TATA
1 TAATATATA
*
171063 TAAT-TATT
1 TAATATATA
171071 TAATA
1 TAATA
171076 ATGGATGGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
8 23 0.66
9 3 0.09
10 9 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TAATATATA
Found at i:171853 original size:15 final size:15
Alignment explanation
Indices: 171767--171850 Score: 52
Period size: 15 Copynumber: 5.8 Consensus size: 15
171757 TCGGGCCGGA
*
171767 TATATATATTTAAAT
1 TATATATATATAAAT
* *
171782 TAAATATATATATAT
1 TATATATATATAAAT
* *
171797 TATATATATTTTTAAT
1 TATATATA-TATAAAT
171813 T-TA-A-AT-TAAAT
1 TATATATATATAAAT
* *
171824 TAAATTTAT-TAATAT
1 TATATATATATAA-AT
171839 TATATATATATA
1 TATATATATATA
171851 TATAATTATT
Statistics
Matches: 51, Mismatches: 12, Indels: 11
0.69 0.16 0.15
Matches are distributed among these distances:
11 5 0.10
12 2 0.04
13 1 0.02
14 6 0.12
15 30 0.59
16 7 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATATAAAT
Found at i:171966 original size:36 final size:36
Alignment explanation
Indices: 171918--171990 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
171908 TTACTAAACT
* * *
171918 CGTCCCCATTTAACATAAACGGTTTTTTCTCGTCCC
1 CGTCCCCATTTAACATAAACAGTTTTTCCACGTCCC
* *
171954 CGTCCCCGTTTAATATAAACAGTTTTTCCACGTCCC
1 CGTCCCCATTTAACATAAACAGTTTTTCCACGTCCC
171990 C
1 C
171991 ATTTAATTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.21, C:0.34, G:0.11, T:0.34
Consensus pattern (36 bp):
CGTCCCCATTTAACATAAACAGTTTTTCCACGTCCC
Found at i:185172 original size:18 final size:19
Alignment explanation
Indices: 185125--185178 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 19
185115 ATGTTTAATG
185125 AAAAAGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
185144 ACAAAATGATATCAATTGTT-
1 A-AAAA-GATATCAATTGTTA
*
185164 AAAAAGATACCAATT
1 AAAAAGATATCAATT
185179 ATTGGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 9 0.28
19 5 0.16
20 5 0.16
21 13 0.41
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (19 bp):
AAAAAGATATCAATTGTTA
Found at i:188027 original size:21 final size:21
Alignment explanation
Indices: 187993--188032 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
187983 AGTCATATCT
*
187993 AGTCGTTGGGGATG-TTTTGG
1 AGTCGTTGGAGATGATTTTGG
188013 AGTCGTTTGGAGATGATTTT
1 AGTCG-TTGGAGATGATTTT
188033 TCTGCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.05, G:0.38, T:0.42
Consensus pattern (21 bp):
AGTCGTTGGAGATGATTTTGG
Found at i:189295 original size:23 final size:23
Alignment explanation
Indices: 189269--189312 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
189259 TGTAATTTAA
189269 ATTT-TATCATATATGTTATTTCC
1 ATTTGTATCATATAT-TTATTTCC
* *
189292 ATTTGTATTATTTATTTATTT
1 ATTTGTATCATATATTTATTT
189313 ATTTATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (23 bp):
ATTTGTATCATATATTTATTTCC
Found at i:189308 original size:4 final size:4
Alignment explanation
Indices: 189299--189323 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
189289 TCCATTTGTA
189299 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
189324 CAATCGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:189837 original size:22 final size:23
Alignment explanation
Indices: 189807--189851 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
189797 TCCCTTATAA
* *
189807 TTTGGTGT-ATTAATCCTCTAAT
1 TTTGGTGTAATAAAACCTCTAAT
*
189829 TTTGTTGTAATAAAACCTCTAAT
1 TTTGGTGTAATAAAACCTCTAAT
189852 CAAAGATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (23 bp):
TTTGGTGTAATAAAACCTCTAAT
Found at i:199853 original size:13 final size:14
Alignment explanation
Indices: 199819--199854 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
199809 ATTTCTATGT
*
199819 AGGGAATTATTTGC
1 AGGGAATTATTTAC
199833 AGGGAATTATTTAC
1 AGGGAATTATTTAC
199847 A-GGAATTA
1 AGGGAATTA
199855 CTCCCCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:200456 original size:3 final size:3
Alignment explanation
Indices: 200448--200498 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
200438 AAACCTTTAA
200448 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
200496 AAT
1 AAT
200499 GGTAAAGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:206952 original size:3 final size:3
Alignment explanation
Indices: 206946--206987 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
206936 AATAATAATA
*
206946 ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
206988 TTCTTTGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:207218 original size:24 final size:24
Alignment explanation
Indices: 207190--207247 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
207180 CGTTAACATG
207190 ATAAACGAACACAAATGAACAAAC
1 ATAAACGAACACAAATGAACAAAC
* **
207214 TTAAACGAACACAAATGAATGAAC
1 ATAAACGAACACAAATGAACAAAC
207238 ATAAACGAAC
1 ATAAACGAAC
207248 TTAAAGGAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.59, C:0.19, G:0.10, T:0.12
Consensus pattern (24 bp):
ATAAACGAACACAAATGAACAAAC
Found at i:208410 original size:5 final size:5
Alignment explanation
Indices: 208373--208531 Score: 55
Period size: 5 Copynumber: 31.6 Consensus size: 5
208363 AATAATAATG
* *
208373 ATAATA ATAAA ATAACA ATAAA AAAGTAA ATAAA AT-AA ACAAA ATAAAA
1 ATAA-A ATAAA ATAA-A ATAAA ATA--AA ATAAA ATAAA ATAAA AT-AAA
* * ** * **
208422 ATAAA GA-AAC AGAAA AT-AA AGCAA AT-AA AT-AA ATAAG AT-AA CCAAA
1 ATAAA -ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
* * * *
208468 ATAAA ATAAA ATAAA AGAAT A-AAA ATAAAA ATAAA GACAACA AAAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA AT-AAA ATAAA -ATAA-A ATAAA
*
208515 ATGAA AT-AA ATAAA ATA
1 ATAAA ATAAA ATAAA ATA
208532 TAGGAAAATA
Statistics
Matches: 116, Mismatches: 22, Indels: 31
0.69 0.13 0.18
Matches are distributed among these distances:
4 23 0.20
5 62 0.53
6 26 0.22
7 5 0.04
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (5 bp):
ATAAA
Found at i:208419 original size:14 final size:14
Alignment explanation
Indices: 208400--208496 Score: 58
Period size: 14 Copynumber: 6.9 Consensus size: 14
208390 ATAAAAAAGT
208400 AAATAAAATAAACA
1 AAATAAAATAAACA
*
208414 AAATAAAAATAAAGA
1 AAAT-AAAATAAACA
*
208429 AACAGAAAATAAAGC-
1 AA-ATAAAATAAA-CA
*
208444 AAAT-AAATAAATA
1 AAATAAAATAAACA
* * *
208457 AGATAACCA-AAATA
1 AAATAA-AATAAACA
208471 AAATAAAATAAA-A
1 AAATAAAATAAACA
*
208484 GAATAAAAATAAA
1 AAAT-AAAATAAA
208497 AATAAAGACA
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
13 15 0.23
14 27 0.42
15 22 0.34
16 1 0.02
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.14
Consensus pattern (14 bp):
AAATAAAATAAACA
Found at i:208425 original size:43 final size:42
Alignment explanation
Indices: 208373--208483 Score: 102
Period size: 43 Copynumber: 2.5 Consensus size: 42
208363 AATAATAATG
* *
208373 ATAATAATAAAATAACAATAAAAAAGTAAATAAAATAAACAAA
1 ATAAAAATAAAATAACAATAAAAAAGCAAAT-AAATAAACAAA
* *
208416 ATAAAAATAAAGA-AACAGA-AAATAAAGCAAATAAATAAATAAG
1 ATAAAAATAAA-ATAACA-ATAAA-AAAGCAAATAAATAAACAAA
208459 ATAACCAAAATAAAATAA-AATAAAA
1 AT-A--AAAATAAAATAACAATAAAA
208484 GAATAAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
43 28 0.50
44 13 0.23
45 5 0.09
46 10 0.18
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (42 bp):
ATAAAAATAAAATAACAATAAAAAAGCAAATAAATAAACAAA
Found at i:208530 original size:9 final size:9
Alignment explanation
Indices: 208382--208598 Score: 61
Period size: 10 Copynumber: 22.8 Consensus size: 9
208372 GATAATAATA
208382 AAATAACAAT
1 AAATAA-AAT
*
208392 AAA-AAAGT
1 AAATAAAAT
208400 AAATAAAAT
1 AAATAAAAT
*
208409 AAACAAAAT
1 AAATAAAAT
208418 AAAAATAAAGA-
1 --AAATAAA-AT
*
208429 AACAGAAAAT
1 AA-ATAAAAT
**
208439 AAAGCAAAT
1 AAATAAAAT
208448 AAAT-AAAT
1 AAATAAAAT
*
208456 AAGATAACCA-
1 AA-ATAA-AAT
208466 AAATAAAAT
1 AAATAAAAT
208475 AAAATAAAA-
1 -AAATAAAAT
*
208484 GAATAAAAAT
1 AAAT-AAAAT
* *
208494 AAAAATAAAG
1 AAATA-AAAT
*
208504 ACAACAAAA-
1 A-AATAAAAT
*
208513 AAATGAAAT
1 AAATAAAAT
208522 AAATAAAAT
1 AAATAAAAT
**
208531 ATAGGAAAAT
1 A-AATAAAAT
*
208541 ATAGTAAAAGT
1 A-AATAAAA-T
*
208552 AATATCCATAAT
1 AA-AT--AAAAT
208564 AAAT-AAAT
1 AAATAAAAT
208572 AAATAAAAGT
1 AAATAAAA-T
**
208582 AAGGAAAACT
1 AAATAAAA-T
208592 AAATAAA
1 AAATAAA
208599 TAATATAGAT
Statistics
Matches: 156, Mismatches: 28, Indels: 46
0.68 0.12 0.20
Matches are distributed among these distances:
8 27 0.17
9 50 0.32
10 57 0.37
11 15 0.10
12 4 0.03
13 3 0.02
ACGTcount: A:0.71, C:0.05, G:0.07, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:208530 original size:61 final size:62
Alignment explanation
Indices: 208389--208531 Score: 140
Period size: 61 Copynumber: 2.4 Consensus size: 62
208379 ATAAAATAAC
*
208389 AATAAAAAAG-TAAATAAAAT-AAACAAAATAAAAATAAAGAAACAGAAAATAAAGCAAATA
1 AATAAATAAGATAAATAAAATAAAACAAAATAAAAATAAAGAAACAGAAAATAAAGCAAATA
** * *
208449 AATAAATAAGATAACCAAAATAAAATAAAATAAAAGA-ATAA-AAATA-AAAATAAAGACAACA-
1 AATAAATAAGATAAATAAAATAAAACAAAATAAAA-ATA-AAGAAACAGAAAATAAAG-CAA-AT
208510 A
62 A
208511 AA-AAATGAA-ATAAATAAAATA
1 AATAAAT-AAGATAAATAAAATA
208532 TAGGAAAATA
Statistics
Matches: 69, Mismatches: 7, Indels: 13
0.78 0.08 0.15
Matches are distributed among these distances:
60 9 0.13
61 31 0.45
62 25 0.36
63 4 0.06
ACGTcount: A:0.75, C:0.05, G:0.06, T:0.15
Consensus pattern (62 bp):
AATAAATAAGATAAATAAAATAAAACAAAATAAAAATAAAGAAACAGAAAATAAAGCAAATA
Found at i:209828 original size:23 final size:25
Alignment explanation
Indices: 209793--209849 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 25
209783 CCTGAAAAAA
* *
209793 ATAATGTAAATAAATGTA-AA-TGT
1 ATAATATAAATAAATGTATAACTAT
*
209816 ATAATATATATAAATGTATAACTAT
1 ATAATATAAATAAATGTATAACTAT
209841 ATAATATAA
1 ATAATATAA
209850 TATTATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 16 0.57
24 2 0.07
25 10 0.36
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (25 bp):
ATAATATAAATAAATGTATAACTAT
Found at i:209829 original size:17 final size:17
Alignment explanation
Indices: 209795--209843 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
209785 TGAAAAAAAT
* *
209795 AATGTA-AATAAATGTA
1 AATGTATAATATATATA
209811 AATGTATAATATATATA
1 AATGTATAATATATATA
209828 AATGTATAACTATATA
1 AATGTATAA-TATATA
209844 ATATAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.21
17 17 0.59
18 6 0.21
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (17 bp):
AATGTATAATATATATA
Found at i:209858 original size:15 final size:15
Alignment explanation
Indices: 209838--209866 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
209828 AATGTATAAC
209838 TATATAATATAATAT
1 TATATAATATAATAT
209853 TATATAATATAATA
1 TATATAATATAATA
209867 ATAACGGACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATAATATAATAT
Found at i:210409 original size:84 final size:84
Alignment explanation
Indices: 210220--211381 Score: 1335
Period size: 84 Copynumber: 13.8 Consensus size: 84
210210 GTTGATAGTC
* * * * *
210220 CCTT-GAGCTGAACGAAATCGAACTCGAAGGT-GTTTGTTGACAGATGACCCTTCTTGCCTTGAG
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
* * *
210283 CTATGCTGTTAATTTGATGTG
66 TTATGCTG-CAA-ATGATGTG
* ** * * *
210304 CCTTTGAGCTGAGTTTAATCGAACTCGAAGGTCTTTTGGTGGCAGATAGCCTTTCTTGCCTTGAG
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
*
210369 CTATGCTGCAAATGATGTG
66 TTATGCTGCAAATGATGTG
** * * * * *
210388 CCTTTAAGCTGAGGGTAATCGAACTCGAAGGTCTTTTGGTGGTAGATAGCCCTTCTTGCCTTCAG
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
*
210453 TTATACTGCAAATGATGTG
66 TTATGCTGCAAATGATGTG
** * * **
210472 CCTTTAAGCTGAGCGCAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAACCTTGAG
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
*
210537 TTATACTGCAAATGATGTG
66 TTATGCTGCAAATGATGTG
* * * * * * *
210556 CCTTGGAGCTGAGCGTAGTCAAACTTGAAGGTATTTTGTTAGCAAATAACCCTTCTTTCCTTGAG
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
* * *
210621 CTATGTTGCAAATGATGTT
66 TTATGCTGCAAATGATGTG
* * * *
210640 CTTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTC-CGACCTTGA
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTG-CCTTGA
*
210704 GTTATGCTACAAATGATGTG
65 GTTATGCTGCAAATGATGTG
* * * * * *
210724 CCTTGCAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTATTGGCAAATAACCCTTCTTACCTTGAG
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
* *
210789 CTATGTTGCAAATGATGTG
66 TTATGCTGCAAATGATGTG
* * * * *
210808 CCTTGGAGTTGAGCGTAGTTGAACGCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAG
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
*
210873 TTATGCTACAAATGATGTG
66 TTATGCTGCAAATGATGTG
* * * * * *
210892 CCTTGAAGCTGAGCGTAATCGAATTCGAAGGTCTTTTATTGGTAGATAGCCCTTCTGGCCTTGAG
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
* * * *
210957 CTATGTTGCAAATGTTGTT
66 TTATGCTGCAAATGATGTG
* * * * * *
210976 CCTTTGAGCTGTGTGTAATCGAACTCGAAGGTCTTTTATTAGCAGATAACCCTTCTAGCCTTGAG
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
*
211041 TTATGTTGCAAATGATGTG
66 TTATGCTGCAAATGATGTG
* * * * * *
211060 CCTTGGAGCTGAGCTTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCATTGAG
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
* *
211125 CTATGTTGCAAATGATGTG
66 TTATGCTGCAAATGATGTG
* * * * * * *
211144 CCTTGCAGCTGAGCGTAGTCAAACTCGAAGTTCTTTTATTGGCAGATAACCCTTCTAGCCTTGAT
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
* * *
211209 TTATGCTGTAATTGATGTA
66 TTATGCTGCAAATGATGTG
* *
211228 CCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCT-CCTTGA
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCT-TGCCTTGA
* *
211292 GTTATGCTACAAATGTTGTG
65 GTTATGCTGCAAATGATGTG
* * *
211312 CCTTTGAGCTGAGTGTAATAGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTT-TTAGCCTTGA
1 CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTT-GCCTTGA
211376 GTTATG
65 GTTATG
211382 TTGCCAATAG
Statistics
Matches: 919, Mismatches: 152, Indels: 14
0.85 0.14 0.01
Matches are distributed among these distances:
82 1 0.00
83 1 0.00
84 858 0.93
85 25 0.03
86 34 0.04
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (84 bp):
CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
TTATGCTGCAAATGATGTG
Found at i:212762 original size:94 final size:95
Alignment explanation
Indices: 212577--212776 Score: 294
Period size: 94 Copynumber: 2.1 Consensus size: 95
212567 CATTGTATAG
* * * * *
212577 ATATTATAGTCACCTTTATCAGGCTAGCTGAATATTATCCACAAACATGGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTAACAGGCTAGCTAAATATTATCCACAAACATCGGGCATTTAACCAATT
*
212642 GCTCTAGAGGGACAACTCAAGTTTTATTGT
66 GCTCTAGAGGGACAACTCAAGCTTTATTGT
* *
212672 ATATTATAATCACCTTTAACAGGCTAGCTAAATCTTATCCATAAA-ATCGGGCATTTAACCAATT
1 ATATTATAATCACCTTTAACAGGCTAGCTAAATATTATCCACAAACATCGGGCATTTAACCAATT
* *
212736 GCTTTAGAGGGACAGCTCAAGCTTTATTGT
66 GCTCTAGAGGGACAACTCAAGCTTTATTGT
212766 ATATATATAAT
1 ATAT-TATAAT
212777 ATTATAATTT
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 48 0.51
95 46 0.49
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (95 bp):
ATATTATAATCACCTTTAACAGGCTAGCTAAATATTATCCACAAACATCGGGCATTTAACCAATT
GCTCTAGAGGGACAACTCAAGCTTTATTGT
Found at i:216783 original size:27 final size:25
Alignment explanation
Indices: 216737--216791 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 25
216727 AAATATAAAG
216737 AAAATAAATAAATAAGATAACCAAAAT
1 AAAATAAATAAATAAGATAA-C-AAAT
216764 AAAATAAA-ATAA-AAGAATAACAAAT
1 AAAATAAATA-AATAAG-ATAACAAAT
216789 AAA
1 AAA
216792 GAGAAGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
25 7 0.27
26 5 0.19
27 14 0.54
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (25 bp):
AAAATAAATAAATAAGATAACAAAT
Found at i:216830 original size:10 final size:10
Alignment explanation
Indices: 216815--216839 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
216805 ATGAAATAAA
216815 TAAAATATAG
1 TAAAATATAG
216825 TAAAATATAG
1 TAAAATATAG
216835 TAAAA
1 TAAAA
216840 GTAATATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (10 bp):
TAAAATATAG
Found at i:218120 original size:23 final size:23
Alignment explanation
Indices: 218071--218127 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
218061 GGCCTAAAAA
* * *
218071 TATAATGTAAATAAATGTAAATG
1 TATAATATATATAAATGTAAATC
*
218094 TATAATATATATAAATGTAGAACTA
1 TATAATATATATAAATGTA-AA-TC
218119 TATAATATA
1 TATAATATA
218128 ATATTATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 17 0.59
24 2 0.07
25 10 0.34
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.37
Consensus pattern (23 bp):
TATAATATATATAAATGTAAATC
Found at i:218122 original size:18 final size:17
Alignment explanation
Indices: 218070--218122 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
218060 AGGCCTAAAA
*
218070 ATAT-AATGTA-AATAA
1 ATATAAATGTAGAATAT
* *
218085 ATGTAAATGTATAATAT
1 ATATAAATGTAGAATAT
218102 ATATAAATGTAGAACTAT
1 ATATAAATGTAGAA-TAT
218120 ATA
1 ATA
218123 ATATAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 3 0.10
16 6 0.19
17 16 0.52
18 6 0.19
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (17 bp):
ATATAAATGTAGAATAT
Found at i:218137 original size:15 final size:15
Alignment explanation
Indices: 218117--218145 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
218107 AATGTAGAAC
218117 TATATAATATAATAT
1 TATATAATATAATAT
218132 TATATAATATAATA
1 TATATAATATAATA
218146 ACGACGGACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATAATATAATAT
Found at i:222084 original size:2 final size:2
Alignment explanation
Indices: 222077--222103 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
222067 TATGTTCATC
222077 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
222104 TCCATACGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:222757 original size:22 final size:21
Alignment explanation
Indices: 222731--222774 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
222721 GCATTAGTAT
*
222731 TTTTAGAATATAGAATGGTTAG
1 TTTTAGAA-ATAGAATGGATAG
*
222753 TTTTAGAACTAGAATGGATAG
1 TTTTAGAAATAGAATGGATAG
222774 T
1 T
222775 GAACCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (21 bp):
TTTTAGAAATAGAATGGATAG
Found at i:225677 original size:20 final size:20
Alignment explanation
Indices: 225652--225706 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
225642 TTTACACTTA
225652 GGGAACCGATTCCCCATAGG
1 GGGAACCGATTCCCCATAGG
225672 GGGAACCGATTCCCCATAGG
1 GGGAACCGATTCCCCATAGG
*
225692 GGGTACCGATTCCCC
1 GGGAACCGATTCCCC
225707 CCAAGCTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (20 bp):
GGGAACCGATTCCCCATAGG
Found at i:228586 original size:15 final size:15
Alignment explanation
Indices: 228568--228620 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
228558 CTTTCATGTC
228568 TTTTTTTTTGAACAG
1 TTTTTTTTTGAACAG
* *
228583 TTTTTTTTCGAACTG
1 TTTTTTTTTGAACAG
*
228598 CTATTTTTTTTCAACA-
1 -T-TTTTTTTTGAACAG
228614 TTTTTTT
1 TTTTTTT
228621 GTGATGGAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 6 0.19
15 14 0.45
16 1 0.03
17 10 0.32
ACGTcount: A:0.17, C:0.11, G:0.08, T:0.64
Consensus pattern (15 bp):
TTTTTTTTTGAACAG
Found at i:234407 original size:33 final size:33
Alignment explanation
Indices: 234370--234432 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
234360 AAATGAAAAT
*
234370 GGATTTTGAA-AATCAAAATGAAATCTTGAAGAA
1 GGATTTAGAACAATCAAAATGAAAT-TTGAAGAA
**
234403 GGATTTAGAACTCTCAAAATGAAATTTGAA
1 GGATTTAGAACAATCAAAATGAAATTTGAA
234433 AGTATTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 14 0.54
34 12 0.46
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (33 bp):
GGATTTAGAACAATCAAAATGAAATTTGAAGAA
Found at i:238326 original size:20 final size:20
Alignment explanation
Indices: 238301--238340 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
238291 TTTTTGTGCA
238301 GAGGGAA-TCGATCCCCCCTT
1 GAGGGAACT-GATCCCCCCTT
*
238321 GAGGGAACTGATTCCCCCTT
1 GAGGGAACTGATCCCCCCTT
238341 TGAAGGGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.23
Consensus pattern (20 bp):
GAGGGAACTGATCCCCCCTT
Found at i:238338 original size:21 final size:23
Alignment explanation
Indices: 238303--238362 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
238293 TTTGTGCAGA
*
238303 GGGAATCGA-TCCCCCCTTG-A-
1 GGGAACCGATTCCCCCCTTGAAG
* *
238323 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTGAAG
238346 GGGAACCGATTCCCCCC
1 GGGAACCGATTCCCCCC
238363 CCACAGGGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 7 0.22
21 9 0.28
22 1 0.03
23 15 0.47
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCTTGAAG
Found at i:243759 original size:20 final size:19
Alignment explanation
Indices: 243736--243780 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
243726 GTGGGACTTA
*
243736 TTTTTTAAAGGGTGTCAATT
1 TTTTTTAAAGAGTGTC-ATT
243756 TTTTTTAAAGAGTGTCATT
1 TTTTTTAAAGAGTGTCATT
243775 TTTTTT
1 TTTTTT
243781 GTTTTTATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.22, C:0.04, G:0.16, T:0.58
Consensus pattern (19 bp):
TTTTTTAAAGAGTGTCATT
Found at i:245840 original size:108 final size:107
Alignment explanation
Indices: 245657--245943 Score: 457
Period size: 108 Copynumber: 2.7 Consensus size: 107
245647 GAACGAAAGA
*
245657 AAGCATCGGTACTTCCGATTTAAGTCGAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTCGAA
1 AAGCATCGGTACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC-TTCGATTCAAGTCGAA
*
245722 CGGAAGGAAGCATCGGTACTTCCGATTCAAGTCGAAAGGAATG
65 CGGAAGGAAGCATCGGTACTTACGATTCAAGTCGAAAGGAATG
* * * *
245765 AAGCATCGGTACTTCCGATTCAAGTCGAAAGGAATGAACCATCGGTACTTACGATTCAAGTCGAA
1 AAGCATCGGTACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTT-CGATTCAAGTCGAA
* *
245830 AGGAATGAAGCATCGGTACTTACGATTCAAGTCGAAAGGAATG
65 CGGAAGGAAGCATCGGTACTTACGATTCAAGTCGAAAGGAATG
* *
245873 AAGCATCGATACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGACACTTCTGATTCAAGTCGAA
1 AAGCATCGGTACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC-GATTCAAGTCGAA
245938 CGGAAG
65 CGGAAG
245944 TATGTATCGC
Statistics
Matches: 161, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
107 3 0.02
108 158 0.98
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.21
Consensus pattern (107 bp):
AAGCATCGGTACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCGATTCAAGTCGAAC
GGAAGGAAGCATCGGTACTTACGATTCAAGTCGAAAGGAATG
Found at i:245940 original size:36 final size:36
Alignment explanation
Indices: 245647--245943 Score: 414
Period size: 36 Copynumber: 8.2 Consensus size: 36
245637 TGATTAAGAA
* * *
245647 GAACGAAAGAAAGCATCGGTACTTCCGATTTAAGTC
1 GAACGGAAGGAAGCATCGGTACTTCCGATTCAAGTC
* *
245683 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGTACTTCCGATTCAAGTC
245719 GAACGGAAGGAAGCATCGGTACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGTACTTCCGATTCAAGTC
* *
245755 GAAAGGAATGAAGCATCGGTACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGTACTTCCGATTCAAGTC
* * * *
245791 GAAAGGAATGAACCATCGGTACTTACGATTCAAGTC
1 GAACGGAAGGAAGCATCGGTACTTCCGATTCAAGTC
* * *
245827 GAAAGGAATGAAGCATCGGTACTTACGATTCAAGTC
1 GAACGGAAGGAAGCATCGGTACTTCCGATTCAAGTC
* * *
245863 GAAAGGAATGAAGCATCGATACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGTACTTCCGATTCAAGTC
** *
245899 GAACGGAAGGAAGCATCGACACTTCTGATTCAAGTC
1 GAACGGAAGGAAGCATCGGTACTTCCGATTCAAGTC
245935 GAACGGAAG
1 GAACGGAAG
245944 TATGTATCGC
Statistics
Matches: 243, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 243 1.00
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGGTACTTCCGATTCAAGTC
Found at i:247765 original size:3 final size:3
Alignment explanation
Indices: 247757--247790 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
247747 AAAATTTCAA
247757 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
247791 TGAACTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:248754 original size:51 final size:51
Alignment explanation
Indices: 248678--248780 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
248668 GTTGCTCTTA
248678 AGAATGATTATCAACAAGTTAGGCTGGAATCTAGTGAAGGGGATGAGTACT
1 AGAATGATTATCAACAAGTTAGGCTGGAATCTAGTGAAGGGGATGAGTACT
*
248729 AGAATGATTATCAACAAGTTGGGCTGGAATCTAGTGAAGGGGATGAGTACT
1 AGAATGATTATCAACAAGTTAGGCTGGAATCTAGTGAAGGGGATGAGTACT
248780 A
1 A
248781 AGCTAGAATG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (51 bp):
AGAATGATTATCAACAAGTTAGGCTGGAATCTAGTGAAGGGGATGAGTACT
Found at i:253565 original size:24 final size:23
Alignment explanation
Indices: 253513--253572 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
253503 GTTTCGGTTT
*
253513 TAAAAAAATCGGTTTTTACCGGA
1 TAAAAAAACCGGTTTTTACCGGA
*
253536 TTAAAAAACCGGTTTTTAATCCGG-
1 TAAAAAAACCGGTTTTT-A-CCGGA
*
253560 TAAAAAATCCGGT
1 TAAAAAAACCGGT
253573 CATCCAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 12 0.39
25 4 0.13
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (23 bp):
TAAAAAAACCGGTTTTTACCGGA
Found at i:255894 original size:48 final size:49
Alignment explanation
Indices: 255792--255900 Score: 152
Period size: 48 Copynumber: 2.2 Consensus size: 49
255782 GATAACCGAA
* *
255792 CCGACCCGACTTATTATAGAACTGAATAAAAATCAAAACTCGAAATGAC
1 CCGACCCGACTTACTATAGAACTGAATAAAAATAAAAACTCGAAATGAC
*
255841 TCGACCCGACTTACTATAG-ACATGAAT-AAAATAAAAA-TCCGAAATGAC
1 CCGACCCGACTTACTATAGAAC-TGAATAAAAATAAAAACT-CGAAATGAC
255889 CCGACCCGACTT
1 CCGACCCGACTT
255901 GAACCTGACT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
47 1 0.02
48 31 0.57
49 22 0.41
ACGTcount: A:0.42, C:0.25, G:0.13, T:0.20
Consensus pattern (49 bp):
CCGACCCGACTTACTATAGAACTGAATAAAAATAAAAACTCGAAATGAC
Found at i:257243 original size:22 final size:23
Alignment explanation
Indices: 257218--257267 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
257208 TAGATTAATT
257218 TTAAAATATAAACATAAA-AATA
1 TTAAAATATAAACATAAAGAATA
* * *
257240 TTAATATTTAAACCTAAAGTAATA
1 TTAAAATATAAACATAAAG-AATA
257264 TTAA
1 TTAA
257268 GTGTCCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 15 0.65
24 8 0.35
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (23 bp):
TTAAAATATAAACATAAAGAATA
Found at i:258672 original size:25 final size:25
Alignment explanation
Indices: 258642--258718 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 25
258632 GATGGAAAAT
258642 GAAAATATAACTAAA-TTTCATCATAA
1 GAAAATATAACTAAACTTTCAT-A-AA
*
258668 -AAAATATCAAGTAAAACTTTCATAAA
1 GAAAATAT-AACT-AAACTTTCATAAA
* *
258694 TGAAAATATAACTAAAATTTAATAA
1 -GAAAATATAACTAAACTTTCATAA
258719 CTTACCAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
25 7 0.17
26 15 0.36
27 7 0.17
28 13 0.31
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (25 bp):
GAAAATATAACTAAACTTTCATAAA
Found at i:263971 original size:2 final size:2
Alignment explanation
Indices: 263964--264035 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
263954 GATAGTTTTA
263964 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
264005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
264036 GTTTAAAGGC
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:264305 original size:20 final size:22
Alignment explanation
Indices: 264268--264308 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
264258 AAAAGCAAAA
264268 ATTAATTTTTTTAAAATAATTAT
1 ATTAATTTTTTT-AAATAATTAT
264291 ATTAA-TTTTTT-AATAATT
1 ATTAATTTTTTTAAATAATT
264309 TTCAACCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTAATTTTTTTAAATAATTAT
Found at i:265207 original size:7 final size:7
Alignment explanation
Indices: 265195--265222 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
265185 TTTCTGATGT
265195 ATTAGTA
1 ATTAGTA
265202 ATTAGTA
1 ATTAGTA
265209 ATTAGTA
1 ATTAGTA
265216 ATTAGTA
1 ATTAGTA
265223 TTCTAGTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (7 bp):
ATTAGTA
Found at i:265809 original size:16 final size:16
Alignment explanation
Indices: 265788--265819 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
265778 ACTATTCACA
*
265788 TGAATAGTGAATTTTG
1 TGAATAGTGAAATTTG
265804 TGAATAGTGAAATTTG
1 TGAATAGTGAAATTTG
265820 GTCGGTGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (16 bp):
TGAATAGTGAAATTTG
Found at i:271590 original size:20 final size:21
Alignment explanation
Indices: 271558--271596 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
271548 CCCAAATTTC
271558 ATACTAGTTCATCCAATATTG
1 ATACTAGTTCATCCAATATTG
271579 ATACTA-TTCATCCAATAT
1 ATACTAGTTCATCCAATAT
271597 CAATACTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (21 bp):
ATACTAGTTCATCCAATATTG
Found at i:271602 original size:20 final size:21
Alignment explanation
Indices: 271558--271603 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
271548 CCCAAATTTC
**
271558 ATACTAGTTCATCCAATATTG
1 ATACTAGTTCATCCAATATCA
271579 ATACTA-TTCATCCAATATCA
1 ATACTAGTTCATCCAATATCA
271599 ATACT
1 ATACT
271604 CGAACCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (21 bp):
ATACTAGTTCATCCAATATCA
Found at i:271820 original size:53 final size:53
Alignment explanation
Indices: 271758--271867 Score: 220
Period size: 53 Copynumber: 2.1 Consensus size: 53
271748 AATGTTATCT
271758 AATCACGAAATCAAGCATAAATCCTAAAGTGCTCAAATACGTAAATCTTAACA
1 AATCACGAAATCAAGCATAAATCCTAAAGTGCTCAAATACGTAAATCTTAACA
271811 AATCACGAAATCAAGCATAAATCCTAAAGTGCTCAAATACGTAAATCTTAACA
1 AATCACGAAATCAAGCATAAATCCTAAAGTGCTCAAATACGTAAATCTTAACA
271864 AATC
1 AATC
271868 TTAATGCTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (53 bp):
AATCACGAAATCAAGCATAAATCCTAAAGTGCTCAAATACGTAAATCTTAACA
Found at i:283382 original size:20 final size:20
Alignment explanation
Indices: 283357--283395 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
283347 GCATCGGGTA
283357 CTGTTCAAACAATATCGGTG
1 CTGTTCAAACAATATCGGTG
283377 CTGTTCAAACAATATCGGT
1 CTGTTCAAACAATATCGGT
283396 ACTATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (20 bp):
CTGTTCAAACAATATCGGTG
Found at i:283410 original size:20 final size:20
Alignment explanation
Indices: 283353--283401 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
283343 TTGAGCATCG
*
283353 GGTACTGTTCAAACAATATC
1 GGTACTATTCAAACAATATC
* *
283373 GGTGCTGTTCAAACAATATC
1 GGTACTATTCAAACAATATC
283393 GGTACTATT
1 GGTACTATT
283402 TATACAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (20 bp):
GGTACTATTCAAACAATATC
Found at i:286076 original size:22 final size:22
Alignment explanation
Indices: 286050--286092 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
286040 AGTTTTAGTA
286050 AAGTTTTCT-CTTTTTACTTTTC
1 AAGTTTTCTCCTTTTT-CTTTTC
*
286072 AAGTTTTTTCCTTTTTCTTTT
1 AAGTTTTCTCCTTTTTCTTTT
286093 ATTTTCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.12, C:0.16, G:0.05, T:0.67
Consensus pattern (22 bp):
AAGTTTTCTCCTTTTTCTTTTC
Found at i:300485 original size:9 final size:9
Alignment explanation
Indices: 300460--300502 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
300450 CACGTGAGAA
300460 TTATTTTATT
1 TTATTTTA-T
300470 CTTATTTTAT
1 -TTATTTTAT
300480 TTATTTTAT
1 TTATTTTAT
*
300489 TTATCTT-T
1 TTATTTTAT
300497 TTATTT
1 TTATTT
300503 ACTGTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
8 6 0.20
9 15 0.50
10 1 0.03
11 8 0.27
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (9 bp):
TTATTTTAT
Found at i:300497 original size:20 final size:21
Alignment explanation
Indices: 300460--300503 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
300450 CACGTGAGAA
300460 TTATTTTATTCTTA-TTTTAT
1 TTATTTTATTCTTATTTTTAT
*
300480 TTATTTTATT-TATCTTTTTAT
1 TTATTTTATTCT-TATTTTTAT
300501 TTA
1 TTA
300504 CTGTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.52
21 9 0.43
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTTTATTCTTATTTTTAT
Found at i:300500 original size:21 final size:22
Alignment explanation
Indices: 300474--300520 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
300464 TTTATTCTTA
*
300474 TTTTATTTA-TTTTATTTATC-T
1 TTTTATTTACTGTT-TTTATCAT
300495 TTTTATTTACTGTTTTTATCAT
1 TTTTATTTACTGTTTTTATCAT
300517 TTTT
1 TTTT
300521 CATTGCCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTACTGTTTTTATCAT
Found at i:302603 original size:73 final size:72
Alignment explanation
Indices: 302466--303052 Score: 922
Period size: 73 Copynumber: 8.0 Consensus size: 72
302456 ACTAAATATT
* *
302466 TTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCCTCAGGGTCATCTGTAAGACCTAC
1 TTTCAAAAAGCCTTCGGGAGCTTTTTGA--TCTT--AAAGCCTCAGGGTCATCTGTAAGACCTAC
302531 AGTGCATGATG
62 AGTGCATGATG
*
302542 TTTCCAAAAAGACTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGT
1 TTT-CAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGT
302607 GCATGATG
65 GCATGATG
***
302615 TTATCAAAAAGCCTTCAAAAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGT
1 TT-TCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGT
302680 GCATGATG
65 GCATGATG
302688 TTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGT
1 -TTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGT
302753 GCATGATG
65 GCATGATG
* *
302761 TTATCAAAAAGCCTTCAGAAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGT
1 TT-TCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGT
302826 GCATGATG
65 GCATGATG
302834 TTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGT
1 -TTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGT
302899 GCATGATG
65 GCATGATG
* * * * * *
302907 TTATCAAAAAGCCTTCAGAAGATTTTTGATCTTATAGCCTTAGGGTCATCTGTAAGGCCTACAGT
1 TT-TCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGT
302972 GCATGATG
65 GCATGATG
* *
302980 TTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTTAGGGTCATCTGTAAGCCCTACAGT
1 -TTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGT
*
303045 GCAAGATG
65 GCATGATG
303053 ATAAGACCTC
Statistics
Matches: 478, Mismatches: 26, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
72 4 0.01
73 437 0.91
74 7 0.01
75 3 0.01
76 3 0.01
77 24 0.05
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (72 bp):
TTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTG
CATGATG
Found at i:303697 original size:39 final size:39
Alignment explanation
Indices: 303650--303726 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
303640 CCCTCCATCC
*
303650 AGCAGCCCCTCCACACATCATTTCCAGCAACTTCCAGCG
1 AGCAGCCCCTCCACACATCAGTTCCAGCAACTTCCAGCG
* * *
303689 AGCAGCCCCTCCACGCATCAGTTGCAGCAGCTTCCAGC
1 AGCAGCCCCTCCACACATCAGTTCCAGCAACTTCCAGC
303727 ACTGCCAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.23, C:0.43, G:0.17, T:0.17
Consensus pattern (39 bp):
AGCAGCCCCTCCACACATCAGTTCCAGCAACTTCCAGCG
Found at i:304858 original size:3 final size:3
Alignment explanation
Indices: 304823--304879 Score: 64
Period size: 3 Copynumber: 19.3 Consensus size: 3
304813 TTTTAATTTC
* * *
304823 ATT ATT TTT AGTT ATT GTT -TT A-T ATT TTT ATT ATT ATT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
304867 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
304880 AAGTATAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:304860 original size:12 final size:13
Alignment explanation
Indices: 304800--304878 Score: 65
Period size: 13 Copynumber: 6.2 Consensus size: 13
304790 AATTACTAGT
*
304800 TTTTTATTTATAA
1 TTTTTATTTATTA
*
304813 TTTTAATTTCATTA
1 TTTTTATTT-ATTA
* *
304827 TTTTTAGTTATTG
1 TTTTTATTTATTA
304840 TTTTATATTT-TTA
1 TTTT-TATTTATTA
*
304853 TTATTA-TTATTA
1 TTTTTATTTATTA
*
304865 TTATTA-TTATTA
1 TTTTTATTTATTA
304877 TT
1 TT
304879 AAAGTATAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
11 2 0.04
12 19 0.35
13 20 0.36
14 14 0.25
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.70
Consensus pattern (13 bp):
TTTTTATTTATTA
Found at i:305156 original size:23 final size:23
Alignment explanation
Indices: 305129--305185 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
305119 ATTTTTGTAA
305129 AATTATAAATTTGAAAATAATAG
1 AATTATAAATTTGAAAATAATAG
305152 AATTATAAATTTGAAAATAATAG
1 AATTATAAATTTGAAAATAATAG
305175 AATTATAAATT
1 AATTATAAATT
305186 AAATATATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTATAAATTTGAAAATAATAG
Found at i:305736 original size:21 final size:20
Alignment explanation
Indices: 305712--305759 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
305702 GGGTTGAATG
305712 CGAAAAAAATAGC-AGTTCGAA
1 CGAAAAAAA-AGCTA-TTCGAA
305733 CGAAAAAAAAGCTATTCGAA
1 CGAAAAAAAAGCTATTCGAA
*
305753 AGAAAAA
1 CGAAAAA
305760 GAAAAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.58, C:0.12, G:0.17, T:0.12
Consensus pattern (20 bp):
CGAAAAAAAAGCTATTCGAA
Found at i:306816 original size:22 final size:22
Alignment explanation
Indices: 306790--306832 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
306780 AGTTTTATTA
306790 AAGTTTTCT-CTTTTTACTTTTC
1 AAGTTTTCTCCTTTTTA-TTTTC
*
306812 AAGTTTTTTCCTTTTTATTTT
1 AAGTTTTCTCCTTTTTATTTT
306833 ATTTTCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.67
Consensus pattern (22 bp):
AAGTTTTCTCCTTTTTATTTTC
Found at i:318132 original size:20 final size:20
Alignment explanation
Indices: 318107--318145 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
318097 TTCGTTTGAT
*
318107 TTTAGAAAATATTTTTTATC
1 TTTAGAAAATAATTTTTATC
318127 TTTAGAAAATAATTTTTAT
1 TTTAGAAAATAATTTTTAT
318146 TTTGAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTAGAAAATAATTTTTATC
Found at i:320516 original size:29 final size:29
Alignment explanation
Indices: 320462--320526 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
320452 AAACATAATT
320462 AAAATAATAAAAACAACAAATAAAAAATA
1 AAAATAATAAAAACAACAAATAAAAAATA
* **
320491 AAAATAGTAAAAAACATTAAAT-AAAAATA
1 AAAATAAT-AAAAACAACAAATAAAAAATA
320520 AAAATAA
1 AAAATAA
320527 AATATGAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.17
Consensus pattern (29 bp):
AAAATAATAAAAACAACAAATAAAAAATA
Found at i:322486 original size:42 final size:41
Alignment explanation
Indices: 322373--322486 Score: 158
Period size: 42 Copynumber: 2.7 Consensus size: 41
322363 GCCCGAAGGT
*
322373 CTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
* * *
322414 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGA
322456 CTTACT-GATGGCCCGAAGGACTTACTCATCA
1 CTTA-TAGATGGCCCGAAGGACTTA-TCATCA
322487 AGAAACCCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 22 0.35
42 40 0.63
43 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
Found at i:322613 original size:71 final size:71
Alignment explanation
Indices: 322523--322822 Score: 485
Period size: 71 Copynumber: 4.2 Consensus size: 71
322513 TTCTTAATTG
* *
322523 TCATCAAAGAACCCCCTACATATCACGTTGGTCCCTCAAGCTTAGTTTCTTATAAATATTCATTG
1 TCATC-AAGAAACCCCTACATATCACGTTGGTCCCTCAAGCTTAGTTTCTTATAAAAATTCATTG
322588 AAAATCA
65 AAAATCA
* *
322595 TCATCAAGAAACCCCTACATATCACGTTGGTCCCTCGAGCTTAGTTTCTTCTAAAAATTCATTGA
1 TCATCAAGAAACCCCTACATATCACGTTGGTCCCTCAAGCTTAGTTTCTTATAAAAATTCATTGA
*
322660 AAATCG
66 AAATCA
* * *
322666 TCATCAAGGAACCCCTACATATCACGTTAGTCCCTCAAGCTTAGTTTCTTATAAAAATTCATTAA
1 TCATCAAGAAACCCCTACATATCACGTTGGTCCCTCAAGCTTAGTTTCTTATAAAAATTCATTGA
322731 AAATCA
66 AAATCA
* * *
322737 TCATCAAGGAACCCCTACATATTACGTTGGTCCCTCGAGCTTAGTTTCTTATAAAAATTCATTG-
1 TCATCAAGAAACCCCTACATATCACGTTGGTCCCTCAAGCTTAGTTTCTTATAAAAATTCATTGA
322801 AAATCA
66 AAATCA
322807 TCATCAAGAAACCCCT
1 TCATCAAGAAACCCCT
322823 GAAAATCAGG
Statistics
Matches: 212, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
70 21 0.10
71 186 0.88
72 5 0.02
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (71 bp):
TCATCAAGAAACCCCTACATATCACGTTGGTCCCTCAAGCTTAGTTTCTTATAAAAATTCATTGA
AAATCA
Found at i:323019 original size:56 final size:57
Alignment explanation
Indices: 322886--323017 Score: 167
Period size: 56 Copynumber: 2.3 Consensus size: 57
322876 TGGTCCCTCG
* * * *
322886 AGCTTAGTTTCTTATAAAAATTCATTGAAAATTGTCATCAAGGAACCCTACATATCA
1 AGCTTAGTTTCTTATAAAAATTCATTGAAAATCGTCATCAAGAAACCCTAAAAATCA
* * **
322943 CG-TTGGTCCCTTATAAAAATTCATTGAAAATCGTCATCAAGAAACCCCTAAAAATCA
1 AGCTTAGTTTCTTATAAAAATTCATTGAAAATCGTCATCAAGAAA-CCCTAAAAATCA
*
323000 AGCTTAGTTTCTTTTAAA
1 AGCTTAGTTTCTTATAAA
323018 TTTTTTTTTG
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
56 37 0.62
57 12 0.20
58 11 0.18
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.33
Consensus pattern (57 bp):
AGCTTAGTTTCTTATAAAAATTCATTGAAAATCGTCATCAAGAAACCCTAAAAATCA
Found at i:324996 original size:13 final size:11
Alignment explanation
Indices: 324959--325022 Score: 66
Period size: 10 Copynumber: 6.2 Consensus size: 11
324949 ATTTGATCGG
324959 TTTTCTCTCTT
1 TTTTCTCTCTT
*
324970 CTTTCT-T-TT
1 TTTTCTCTCTT
*
324979 TTTCTCTCTCTC
1 TTT-TCTCTCTT
324991 TTTTCTCTC-T
1 TTTTCTCTCTT
325001 TTTT-TCTCTT
1 TTTTCTCTCTT
325011 TTTTCTCT-TT
1 TTTTCTCTCTT
325021 TT
1 TT
325023 CTGTGTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
9 8 0.18
10 17 0.39
11 15 0.34
12 4 0.09
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTCTCTCTT
Found at i:324996 original size:25 final size:24
Alignment explanation
Indices: 324962--325009 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
324952 TGATCGGTTT
*
324962 TCTCTCTTCTTTCTTTTTTTCTCTC
1 TCTCTCTTCTCTC-TTTTTTCTCTC
*
324987 TCTCTTTTCTCTCTTTTTTCTCT
1 TCTCTCTTCTCTCTTTTTTCTCT
325010 TTTTTCTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (24 bp):
TCTCTCTTCTCTCTTTTTTCTCTC
Found at i:325022 original size:9 final size:9
Alignment explanation
Indices: 324959--325040 Score: 66
Period size: 9 Copynumber: 9.6 Consensus size: 9
324949 ATTTGATCGG
*
324959 TTTTCTCTC
1 TTTTTTCTC
*
324968 TTCTTTCT-
1 TTTTTTCTC
324976 TTTTTTCTC
1 TTTTTTCTC
*
324985 ---TCTCTC
1 TTTTTTCTC
*
324991 TTTTCTCTC
1 TTTTTTCTC
325000 TTTTTTCTC
1 TTTTTTCTC
325009 TTTTTTCTC
1 TTTTTTCTC
*
325018 -TTTTTCTG
1 TTTTTTCTC
*
325026 TGTTTTTTTC
1 T-TTTTTCTC
325036 TTTTT
1 TTTTT
325041 CTTTTTCCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
6 5 0.08
8 14 0.24
9 33 0.56
10 7 0.12
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:325040 original size:18 final size:17
Alignment explanation
Indices: 324959--325046 Score: 76
Period size: 18 Copynumber: 5.2 Consensus size: 17
324949 ATTTGATCGG
*
324959 TTTTCTCTCTTCTTTCT-
1 TTTTTTCTCTT-TTTCTC
*
324976 TTTTTTCTC--TCTCTC
1 TTTTTTCTCTTTTTCTC
*
324991 TTTTCTCTCTTTTTTCTC
1 TTTTTTCTC-TTTTTCTC
*
325009 TTTTTTCTCTTTTTCTG
1 TTTTTTCTCTTTTTCTC
*
325026 TGTTTTTTTCTTTTTCT-
1 T-TTTTTCTCTTTTTCTC
325043 TTTT
1 TTTT
325047 CCTTTTTCGT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
14 4 0.07
15 8 0.14
16 3 0.05
17 17 0.29
18 27 0.46
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTTCTCTTTTTCTC
Found at i:325044 original size:33 final size:35
Alignment explanation
Indices: 325002--325087 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 35
324992 TTTCTCTCTT
325002 TTTTCTCTTTTTTCTCTTTTTC-TGTGT-TTTTTTC
1 TTTT-TCTTTTTTCTCTTTTTCGTGTGTATTTTTTC
325036 TTTTTC-TTTTTC-CTTTTTCGTGTGTATTTTTTC
1 TTTTTCTTTTTTCTCTTTTTCGTGTGTATTTTTTC
*
325069 TATATCTCTTCTTTTCTCT
1 T-T-TTTCTT-TTTTCTCT
325088 CTGTGTTGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
31 7 0.16
32 11 0.25
33 10 0.23
34 5 0.11
35 3 0.07
36 1 0.02
37 5 0.11
38 2 0.05
ACGTcount: A:0.03, C:0.19, G:0.06, T:0.72
Consensus pattern (35 bp):
TTTTTCTTTTTTCTCTTTTTCGTGTGTATTTTTTC
Found at i:333552 original size:19 final size:19
Alignment explanation
Indices: 333525--333591 Score: 116
Period size: 19 Copynumber: 3.5 Consensus size: 19
333515 TGGAATTTTC
*
333525 TGAAGTCGATTTAAGTGAA
1 TGAAATCGATTTAAGTGAA
333544 TGAAATCGATTTAAGTGAA
1 TGAAATCGATTTAAGTGAA
*
333563 TGAAATCTATTTAAGTGAA
1 TGAAATCGATTTAAGTGAA
333582 TGAAATCGAT
1 TGAAATCGAT
333592 AATTGTAGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (19 bp):
TGAAATCGATTTAAGTGAA
Found at i:343489 original size:7 final size:7
Alignment explanation
Indices: 343477--343514 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
343467 GTCAAAGAAA
343477 GTCAACG
1 GTCAACG
343484 GTCAACG
1 GTCAACG
343491 GTCAACG
1 GTCAACG
343498 GTCAACG
1 GTCAACG
343505 GTCAACG
1 GTCAACG
343512 GTC
1 GTC
343515 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:343536 original size:22 final size:22
Alignment explanation
Indices: 343504--343551 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
343494 AACGGTCAAC
*
343504 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAAAGGTCGGGTCGGGTCG
343526 GGTCAAAGGTCGGGTCGGGTCG
1 GGTCAAAGGTCGGGTCGGGTCG
343548 GGTC
1 GGTC
343552 GGTCGGGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.10, C:0.21, G:0.50, T:0.19
Consensus pattern (22 bp):
GGTCAAAGGTCGGGTCGGGTCG
Found at i:343557 original size:4 final size:5
Alignment explanation
Indices: 343511--343560 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
343501 AACGGTCAAC
*
343511 GGTCG GGTCG GGTCG GGTCAAA GGTCG GGTCG GGTCG GGTC- GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
343561 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 4 0.10
5 32 0.80
7 4 0.10
ACGTcount: A:0.06, C:0.20, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:350784 original size:20 final size:20
Alignment explanation
Indices: 350761--350813 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
350751 TTGAAATTTC
* *
350761 ATTAAAACTTTTGAAAAAAA
1 ATTAAAAATTATGAAAAAAA
**
350781 ATTAAAAATTATGAAAAAGT
1 ATTAAAAATTATGAAAAAAA
350801 ATTATAAAATTAT
1 ATTA-AAAATTAT
350814 ATCAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (20 bp):
ATTAAAAATTATGAAAAAAA
Found at i:354822 original size:12 final size:11
Alignment explanation
Indices: 354797--354829 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
354787 CAATTTTGGG
354797 TAAATAAA-AA
1 TAAATAAATAA
354807 TAAATAAATTAA
1 TAAATAAA-TAA
354819 TAAATAAATAA
1 TAAATAAATAA
354830 ACCCACCCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.38
11 3 0.14
12 10 0.48
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:358422 original size:151 final size:151
Alignment explanation
Indices: 358148--358450 Score: 606
Period size: 151 Copynumber: 2.0 Consensus size: 151
358138 TACCAATTGG
358148 ATAGTTATGATTATGAATTGCTTTAAGGGCATAAAACACTAAAATACTAGTAAGATCTTGCATAA
1 ATAGTTATGATTATGAATTGCTTTAAGGGCATAAAACACTAAAATACTAGTAAGATCTTGCATAA
358213 CATTTTAGGAGAGAGAACGAATGAGATGTAGTGGGTGAGGGAACGATCTCACCTACTTATATTGT
66 CATTTTAGGAGAGAGAACGAATGAGATGTAGTGGGTGAGGGAACGATCTCACCTACTTATATTGT
358278 AGTTAATGATAATGATAAGAT
131 AGTTAATGATAATGATAAGAT
358299 ATAGTTATGATTATGAATTGCTTTAAGGGCATAAAACACTAAAATACTAGTAAGATCTTGCATAA
1 ATAGTTATGATTATGAATTGCTTTAAGGGCATAAAACACTAAAATACTAGTAAGATCTTGCATAA
358364 CATTTTAGGAGAGAGAACGAATGAGATGTAGTGGGTGAGGGAACGATCTCACCTACTTATATTGT
66 CATTTTAGGAGAGAGAACGAATGAGATGTAGTGGGTGAGGGAACGATCTCACCTACTTATATTGT
358429 AGTTAATGATAATGATAAGAT
131 AGTTAATGATAATGATAAGAT
358450 A
1 A
358451 ATCACATGAT
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 152 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (151 bp):
ATAGTTATGATTATGAATTGCTTTAAGGGCATAAAACACTAAAATACTAGTAAGATCTTGCATAA
CATTTTAGGAGAGAGAACGAATGAGATGTAGTGGGTGAGGGAACGATCTCACCTACTTATATTGT
AGTTAATGATAATGATAAGAT
Found at i:360741 original size:20 final size:20
Alignment explanation
Indices: 360718--360785 Score: 136
Period size: 20 Copynumber: 3.4 Consensus size: 20
360708 AGTTTCCAAT
360718 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
360738 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
360758 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
360778 TTCGCAAC
1 TTCGCAAC
360786 TGAATTTCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
TTCGCAACGCGATAGTCAAA
Found at i:360797 original size:19 final size:19
Alignment explanation
Indices: 360773--360842 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
360763 AACGCGATAG
360773 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
360792 TCAAATTCGCAAATGAATT
1 TCAAATTCGCAACTGAATT
*
360811 TCAAATTCGCAACGCGAATT
1 TCAAATTCGCAAC-TGAATT
*
360831 T-AATTTCGCAAC
1 TCAAATTCGCAAC
360843 AGGTTTTAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 40 0.87
20 6 0.13
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.30
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:360831 original size:20 final size:20
Alignment explanation
Indices: 360674--360842 Score: 127
Period size: 20 Copynumber: 8.6 Consensus size: 20
360664 AAATGACCAA
* *
360674 CAAATTCGCAACACGAATTC
1 CAAATTCGCAACGCGAATTT
* * * *
360694 CAATTTTGCAAC-CCAGTTT
1 CAAATTCGCAACGCGAATTT
* *
360713 CCAATTTCGCAACGCG-ATAGT
1 -CAAATTCGCAACGCGAAT-TT
*
360734 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-TT
*
360754 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-TT
*
360774 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
**
360793 CAAATTCGCAA-ATGAATTT
1 CAAATTCGCAACGCGAATTT
360812 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
360832 -AATTTCGCAAC
1 CAAATTCGCAAC
360843 AGGTTTTAGT
Statistics
Matches: 128, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
19 45 0.35
20 81 0.63
21 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:361757 original size:24 final size:24
Alignment explanation
Indices: 361700--361746 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
361690 AGTCAGTATT
*
361700 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
361724 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
361747 TTGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:364356 original size:20 final size:20
Alignment explanation
Indices: 364333--364376 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
364323 CGATCAACAC
*
364333 GAAAGTCAAATTCGCAACGT
1 GAAAGTCAAATTCGCAACGA
364353 GAAAGTCAAATTCGCAACGA
1 GAAAGTCAAATTCGCAACGA
364373 GAAA
1 GAAA
364377 TAAGTGTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.16
Consensus pattern (20 bp):
GAAAGTCAAATTCGCAACGA
Found at i:364451 original size:20 final size:20
Alignment explanation
Indices: 364426--364541 Score: 196
Period size: 20 Copynumber: 5.8 Consensus size: 20
364416 ATTCGCAAAC
*
364426 CGAATTTGACTATCACGTAG
1 CGAATTTGACTATCGCGTAG
364446 CGAATTTGACTATCGCGTAG
1 CGAATTTGACTATCGCGTAG
364466 CGAATTTGACTATCGCGTAG
1 CGAATTTGACTATCGCGTAG
364486 CGAATTTGACTATCGCGTAG
1 CGAATTTGACTATCGCGTAG
* * *
364506 CGCATTTGACTTTCGCGTTG
1 CGAATTTGACTATCGCGTAG
364526 CGAATTTGACTATCGC
1 CGAATTTGACTATCGC
364542 AACGCTTATT
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 90 1.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (20 bp):
CGAATTTGACTATCGCGTAG
Found at i:364559 original size:34 final size:38
Alignment explanation
Indices: 364431--364566 Score: 136
Period size: 40 Copynumber: 3.6 Consensus size: 38
364421 CAAACCGAAT
* * * * *
364431 TTGACTATCACGTAGCGAATTTGACTATCGCGTAGCGAA
1 TTGACTTTCGCGTTGCGAATTTGACTATCGCG-AACGCA
* * *
364470 TTTGACTATCGCGTAGCGAATTTGACTATCGCGTAGCGCA
1 -TTGACTTTCGCGTTGCGAATTTGACTATCGCG-AACGCA
364510 TTTGACTTTCGCGTTGCGAATTTGACTATCGC-AACGC-
1 -TTGACTTTCGCGTTGCGAATTTGACTATCGCGAACGCA
364547 TT-A-TTTCGCGTTGCGAATTT
1 TTGACTTTCGCGTTGCGAATTT
364567 ACCTTCAATG
Statistics
Matches: 91, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
34 17 0.19
35 1 0.01
36 2 0.02
38 4 0.04
40 67 0.74
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (38 bp):
TTGACTTTCGCGTTGCGAATTTGACTATCGCGAACGCA
Found at i:364671 original size:25 final size:25
Alignment explanation
Indices: 364633--364682 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
364623 AAATCAATTA
*
364633 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
364658 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
364683 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:365435 original size:39 final size:39
Alignment explanation
Indices: 365392--365478 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
365382 TCCGATGCTC
* *
365392 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGAAA
* *
365431 ATCAAAATTAAAATCTCATATGGTGCCAAGCAAAAGAAA
1 ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGAAA
365470 ATCAAAATC
1 ATCAAAATC
365479 TACAACTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGAAA
Found at i:365723 original size:20 final size:20
Alignment explanation
Indices: 365658--365713 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
365648 TGCGATCAAT
* * *
365658 GCGAAAGTTAAATTCACAAC
1 GCGAAAGTCAAATTCGCAAA
365678 GTC-AAAGTCAAATTCGCAAA
1 G-CGAAAGTCAAATTCGCAAA
365698 GCGAAAGTCAAATTCG
1 GCGAAAGTCAAATTCG
365714 TAAACTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.20
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAA
Found at i:365902 original size:14 final size:14
Alignment explanation
Indices: 365868--365921 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
365858 ATAATTCTTA
*
365868 TTTACAAATCAAAT
1 TTTACAAATCAACT
**
365882 TAAACAAATCAACT
1 TTTACAAATCAACT
*
365896 TTTACAAATCATCT
1 TTTACAAATCAACT
365910 TTTACAAATCAA
1 TTTACAAATCAA
365922 TTAATCAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (14 bp):
TTTACAAATCAACT
Found at i:367322 original size:21 final size:21
Alignment explanation
Indices: 367298--367397 Score: 98
Period size: 21 Copynumber: 4.8 Consensus size: 21
367288 GGCGGGACCA
367298 CTTGAACGATGATAGGGGCCT
1 CTTGAACGATGATAGGGGCCT
* *
367319 CTTGAGCGATG-TGAGGGGCTT
1 CTTGAACGATGAT-AGGGGCCT
* *
367340 CTTCG-ATGATGAGAGGGGCCT
1 CTT-GAACGATGATAGGGGCCT
*
367361 CTTGAACGATAGA-AGGCGCCT
1 CTTGAACGAT-GATAGGGGCCT
*
367382 CTTGAATGATGATAGG
1 CTTGAACGATGATAGG
367398 TGCATCGGGC
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
20 4 0.06
21 57 0.89
22 3 0.05
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.25
Consensus pattern (21 bp):
CTTGAACGATGATAGGGGCCT
Found at i:369600 original size:19 final size:20
Alignment explanation
Indices: 369578--369617 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
369568 AAAATCGCAA
369578 TGCGA-TTTTAGTTTCGCGT
1 TGCGATTTTTAGTTTCGCGT
*
369597 TGCGATTTTTATTTTCGCGT
1 TGCGATTTTTAGTTTCGCGT
369617 T
1 T
369618 CTGAATTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.10, C:0.15, G:0.23, T:0.53
Consensus pattern (20 bp):
TGCGATTTTTAGTTTCGCGT
Found at i:369905 original size:22 final size:22
Alignment explanation
Indices: 369877--369949 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
369867 GATGGAGATA
369877 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAAATGGG
*
369899 GACGGATTTCGTCGAAAATGGG
1 GACGGATTTCGTCGGAAATGGG
* *
369921 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAAATGGG
369943 GACGGAT
1 GACGGAT
369950 GTCGCCGTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.23, C:0.12, G:0.41, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATGGG
Found at i:379604 original size:30 final size:30
Alignment explanation
Indices: 379568--379631 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
379558 GAAGGACCTG
* *
379568 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
379598 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
379628 TCCA
1 TCCA
379632 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:381062 original size:2 final size:2
Alignment explanation
Indices: 381057--381129 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
381047 CATCCTTATC
381057 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
381099 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
381130 CATTATTTAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:391130 original size:22 final size:22
Alignment explanation
Indices: 391059--391131 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
391049 GTGCCTTAGC
* * *
391059 ATTGATACCAAAGTCCCTCGAC
1 ATTGATACCAAAGTGCATCGAT
**
391081 ATTGATACGGAAGTGCATTCG-T
1 ATTGATACCAAAGTGCA-TCGAT
* *
391103 ACTGATACTAAAGTGCATCGAT
1 ATTGATACCAAAGTGCATCGAT
391125 ATTGATA
1 ATTGATA
391132 TGAACGTTCA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 3 0.08
22 34 0.85
23 3 0.08
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (22 bp):
ATTGATACCAAAGTGCATCGAT
Found at i:393311 original size:18 final size:18
Alignment explanation
Indices: 393288--393394 Score: 160
Period size: 18 Copynumber: 5.9 Consensus size: 18
393278 GCGTAGAATT
*
393288 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
393306 TGTCCCGAAGGACCATTG
1 TGTCCCGAAGGACCACTA
393324 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
393342 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* **
393360 TGTCCCGAATGACTGCTA
1 TGTCCCGAAGGACCACTA
393378 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
393395 GATAATCCCT
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 78 1.00
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:404183 original size:21 final size:21
Alignment explanation
Indices: 404159--404208 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
404149 GGAAGGAAAG
404159 GGAGAAACTTTGTTTTTGGTA
1 GGAGAAACTTTGTTTTTGGTA
404180 GGAGAAACTTTGTTTTTGGTA
1 GGAGAAACTTTGTTTTTGGTA
404201 GGAGAAAC
1 GGAGAAAC
404209 AAATTGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.06, G:0.30, T:0.36
Consensus pattern (21 bp):
GGAGAAACTTTGTTTTTGGTA
Found at i:409304 original size:30 final size:30
Alignment explanation
Indices: 409270--409356 Score: 74
Period size: 29 Copynumber: 2.9 Consensus size: 30
409260 ACACAAAATA
*
409270 TTTTAATATATTTTATTTTCATCATTGAT-T
1 TTTTAATATATTTTATTTT-ATAATTGATAT
* * *
409300 TTTTAAAAAATTATT-TTTTATTATT-ATAT
1 TTTTAATATATT-TTATTTTATAATTGATAT
409329 TTTTAAT-TCATTTTATTTTGATAATTGA
1 TTTTAATAT-ATTTTATTTT-ATAATTGA
409357 GTCATTAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
28 4 0.09
29 19 0.42
30 19 0.42
31 3 0.07
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTTAATATATTTTATTTTATAATTGATAT
Found at i:415492 original size:6 final size:6
Alignment explanation
Indices: 415481--415508 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
415471 ATATTTTATC
415481 TTAACA TTAACA TTAACA TTAACA TTAA
1 TTAACA TTAACA TTAACA TTAACA TTAA
415509 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
TTAACA
Found at i:415567 original size:39 final size:39
Alignment explanation
Indices: 415513--415605 Score: 159
Period size: 39 Copynumber: 2.4 Consensus size: 39
415503 CATTAAAAAT
**
415513 AAAAATATAACTTTATTTTTATGCATTTAAAATATATTG
1 AAAAATATATTTTTATTTTTATGCATTTAAAATATATTG
*
415552 AAAAATATGTTTTTATTTTTATGCATTTAAAATATATTG
1 AAAAATATATTTTTATTTTTATGCATTTAAAATATATTG
415591 AAAAATATATTTTTA
1 AAAAATATATTTTTA
415606 ATGTTAAGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (39 bp):
AAAAATATATTTTTATTTTTATGCATTTAAAATATATTG
Found at i:415630 original size:18 final size:18
Alignment explanation
Indices: 415609--415698 Score: 65
Period size: 18 Copynumber: 4.8 Consensus size: 18
415599 ATTTTTAATG
415609 TTAAGATATGAATTAAAT
1 TTAAGATATGAATTAAAT
*
415627 TTAATATATGAATTTAACAT
1 TTAAGATATGAA-TTAA-AT
** * * *
415647 ACAAAATAT-ATTCTTTAAT
1 TTAAGATATGA--ATTAAAT
415666 GTTAAGATATGAATTAAAT
1 -TTAAGATATGAATTAAAT
*
415685 TTAACATATGAATT
1 TTAAGATATGAATT
415699 TAAGATAAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
18 24 0.44
19 12 0.22
20 17 0.31
21 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (18 bp):
TTAAGATATGAATTAAAT
Found at i:415664 original size:58 final size:56
Alignment explanation
Indices: 415591--415711 Score: 206
Period size: 58 Copynumber: 2.1 Consensus size: 56
415581 AAATATATTG
*
415591 AAAAATATATTTTTAATGTTAAGATATGAATTAAATTTAATATATGAATTTAACAT
1 AAAAATATATTTTTAATGTTAAGATATGAATTAAATTTAACATATGAATTTAACAT
*
415647 ACAAAATATATTCTTTAATGTTAAGATATGAATTAAATTTAACATATGAATTTAAGAT
1 A-AAAATATATT-TTTAATGTTAAGATATGAATTAAATTTAACATATGAATTTAACAT
415705 AAAAATA
1 AAAAATA
415712 AACTTTATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
56 1 0.02
57 16 0.26
58 44 0.72
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (56 bp):
AAAAATATATTTTTAATGTTAAGATATGAATTAAATTTAACATATGAATTTAACAT
Found at i:416788 original size:37 final size:37
Alignment explanation
Indices: 416702--416802 Score: 121
Period size: 37 Copynumber: 2.7 Consensus size: 37
416692 TTCGTCCTAT
* **
416702 TATGATTCAAACTCCTAAAAATAGGATAAAATTTTGT
1 TATGATTCAAACTCCTAAAAATAGGATAAAATTCTAC
* * * *
416739 TAGGATTCAAACTCTTAAAAATAGGATAGAGTTCTAC
1 TATGATTCAAACTCCTAAAAATAGGATAAAATTCTAC
* *
416776 TATGATTTAAACTCCTAAAGATAGGAT
1 TATGATTCAAACTCCTAAAAATAGGAT
416803 CCACAAGCAC
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.33
Consensus pattern (37 bp):
TATGATTCAAACTCCTAAAAATAGGATAAAATTCTAC
Found at i:417409 original size:2 final size:2
Alignment explanation
Indices: 417402--417436 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
417392 ATATTATTAC
417402 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
417437 TGTAATTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:417686 original size:4 final size:4
Alignment explanation
Indices: 417673--417702 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
417663 TATATATTAA
417673 TATT TCATT TATT TATT TATT TATT TATT T
1 TATT T-ATT TATT TATT TATT TATT TATT T
417703 TTCCTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:422210 original size:16 final size:17
Alignment explanation
Indices: 422189--422274 Score: 70
Period size: 19 Copynumber: 4.8 Consensus size: 17
422179 ATTCAATCAT
422189 AACAAAAAGAAAA-AAA
1 AACAAAAAGAAAACAAA
*
422205 AACAAAAAAGAAAAGAAGCA
1 AAC-AAAAAGAAAACAA--A
422225 AA-AAAGAAGAAAACAAA
1 AACAAA-AAGAAAACAAA
422242 AGA-AAAAAGAAAGAACAAA
1 A-ACAAAAAG-AA-AACAAA
422261 AATCAAAAAGAAAA
1 AA-CAAAAAGAAAA
422275 GGGACAAAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
16 3 0.05
17 15 0.25
18 14 0.24
19 18 0.31
20 9 0.15
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.01
Consensus pattern (17 bp):
AACAAAAAGAAAACAAA
Found at i:422237 original size:24 final size:22
Alignment explanation
Indices: 422193--422249 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
422183 AATCATAACA
*
422193 AAAAGAAAAAAAAACAAAAAAG
1 AAAAGAAAAAAAAACAAAAAAC
* *
422215 AAAAGAAGCAAAAAAGAAGAAAAC
1 AAAAGAA-AAAAAAACAA-AAAAC
422239 AAAAGAAAAAA
1 AAAAGAAAAAA
422250 GAAAGAACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 7 0.24
23 11 0.38
24 11 0.38
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAAAAACAAAAAAC
Found at i:422248 original size:36 final size:34
Alignment explanation
Indices: 422195--422262 Score: 100
Period size: 36 Copynumber: 1.9 Consensus size: 34
422185 TCATAACAAA
422195 AAGAAAAAAAAACAAAAAAGAAAAGAAGCAAAAAAG
1 AAGAAAAAAAAACAAAAAAG-AAAGAA-CAAAAAAG
* *
422231 AAGAAAACAAAAGAAAAAAGAAAGAACAAAAA
1 AAGAAAAAAAAACAAAAAAGAAAGAACAAAAA
422263 TCAAAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 6 0.20
35 6 0.20
36 18 0.60
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (34 bp):
AAGAAAAAAAAACAAAAAAGAAAGAACAAAAAAG
Done.